BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063523.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 4,713,401 number of mapped reads = 4,432,094 (94.03%) number of supplementary alignments = 29,048 (0.62%) number of secondary alignments = 0 number of mapped bases = 284,345,515 bp number of sequenced bases = 284,224,720 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 579,313 duplication rate = 10.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6793 >>>>>>> ACTG content number of A's = 73,172,804 bp (25.74%) number of C's = 51,464,427 bp (18.11%) number of T's = 92,034,034 bp (32.38%) number of G's = 67,521,750 bp (23.76%) number of N's = 31,705 bp (0.01%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,538,327 number of insertions = 17,435 mapped reads with insertion percentage = 0.39% number of deletions = 68,834 mapped reads with deletion percentage = 1.54% homopolymer indels = 44.04% >>>>>>> Coverage mean coverageData = 0.0919X std coverageData = 0.8831X There is a 6.5% of reference with a coverageData >= 1X There is a 1.72% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 28119533 0.11281630066630807 1.953018257279479 chr2 243199373 30873585 0.12694763403029002 1.5180147430380946 chr3 198022430 17391614 0.08782648511080285 0.3973639318408608 chr4 191154276 13789901 0.07214016494195505 0.38953452182166154 chr5 180915260 14841388 0.08203502567997857 0.3848760872943165 chr6 171115067 18390566 0.10747484907334315 0.6076047980181509 chr7 159138663 20855836 0.13105448799704947 0.9156047580451572 chr8 146364022 12072291 0.08248127398412158 0.821534567619553 chr9 141213431 7904914 0.055978485502558184 0.5688761483353136 chr10 135534747 14511188 0.10706618281435977 0.5799939956001272 chr11 135006516 14061422 0.10415365433176574 0.5757878565016532 chr12 133851895 11143259 0.08325066298090139 0.4054963105358216 chr13 115169878 6615140 0.057438108947202325 0.36407826909910407 chr14 107349540 4609683 0.04294087333769665 0.33378658007459217 chr15 102531392 5092176 0.049664555417330135 0.3951245341843703 chr16 90354753 5936986 0.06570751181180252 0.37549604735501146 chr17 81195210 8214784 0.1011732588658863 0.4641154130225753 chr18 78077248 6914881 0.08856460975673733 1.0936517543649895 chr19 59128983 6703196 0.11336565690636012 1.23443363916064 chr20 63025520 4539908 0.07203285272378554 0.3794687504763852 chr21 48129895 4528781 0.09409496945713262 0.43103435123414036 chr22 51304566 3291481 0.06415571276833333 0.3356613688990668 chrMT 16571 435307 26.2692052380665 13.98994356177153 chrX 155270560 22791773 0.14678747213895538 0.6100461339504734 chrY 59373566 715922 0.012057924902135742 0.34478096250293966